Berberis koreana is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth. This was followed by full-length cDNA sequencing analysis using the PacBio sequencer platform to determine the number of isoforms of those expressed genes. We identified 23,246 full-length unigenes, among which 8,479 had more than one isoform. The number of isoforms ranged between two to thirty-one among all genes. Complete isoform analysis was carried out on the unigenes encoding BIA synthesis. Thirteen of the sixteen genes encoding enzymes for berberine synthesis were present in more than one copy. This demonstrates that gene duplication and translation into isoforms may contribute to the functional specificity of the duplicated genes and isoforms in plant alkaloid synthesis. Our study also demonstrated the streamlining of berberine biosynthesis via the absence of genes for enzymes of other BIAs, but the presence of all the genes for berberine biosynthesize in B. koreana. In addition to genes encoding enzymes for the berberine biosynthesis pathway, the genes encoding enzymes for other BIAs were not present in our dataset except for those encoding corytuberine synthase (CTS) and berbamunine synthase (BS). Therefore, this explains how B. koreana produces berberine by blocking the pathways leading to other BIAs, effectively only allowing the pathway to lead to berberine synthesis.

High-throughput RNA sequencing has revolutionized transcriptome-based studies of candidate genes, key pathways and gene regulation in non-model organisms. We analyzed full-length cDNA sequences in Zanthoxylum planispinum (Z. planispinum), a medicinal herb in major parts of East Asia. The full-length mRNA derived from tissues of leaf, early fruit and maturing fruit stage were sequenced using PacBio RSII platform to identify isoform transcriptome. We obtained 51,402 unigenes, with average 1781 bp per gene in 82.473 Mb gene lengths. Among 51,402, 3963 unigenes showed variety of isoform. By selection of one representative gene among each of the various isoforms, we finalized 46,306 unique gene set for this herb. We identified 76 cytochrome P450 (CYP450) and related isoforms that are of the wide diversity in the molecular function and biological process. These transcriptome data of Z. planispinum will provide a good resource to study metabolic engineering for the production of valuable medicinal drugs and phytochemicals.

Variation is the primary source for plant and animal breeding and evolution, and hence, the detection of variation is an integral part of genetics, breeding, and ecology. Various molecular marker systems have been developed to detect genetic variation. They detect sequence variations (e.g., restriction fragment length polymorphism, randomly amplified polymorphic DNA, amplified fragment length polymorphism) or simple sequence motif variations. However, a large portion of genomic variation is derived from the transposition of transposable elements (TEs), which are major denizens of most eukaryote genomes. Therefore, molecular markers derived from TEs are valuable resources for dissecting genomes in plants and animals. Because class I retrotransposons transpose by a ''copy-and-paste'' semi-conservative manner, retrotransposon-based markers (e.g., Inter-retrotransposon amplified polymorphism, retrotransposon-microsatellite amplified polymorphism, sequence-specific amplified polymorphism) can reveal highly accurate phylogenetic relationships among related taxa as well as among accessions within a species. Transposon display based on class II DNA transposons has also been used in various genetics fields. A large amount of fairly accurate genome sequences are now being generated, and computational biology allows us to mine the TEs on a genome-wide scale. Thus, TE-based molecular markers are adding another venue to the other marker systems used for the molecular dissection of genomes.

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